I'm not entirely sure what has changed recently with that section. I've sent a message off to a few of the guys who might have worked in this area recently, they should get back to you within a few days.

I did a few experiments and it seems the API has changed. It used to be if you do not pass the line items to the fulfillment API, it will just fulfill everything for that order. Now it seems the line items have to be explicitly passed in in order to fulfill an order.